Research Associate

College of Life Sciences
Zhejiang University

Hangzhou, China

2025 - 2023

Research Assistant

School of Biomedical Engineering
Tianjin Medical University

Tianjin, China

2017 - 2016

Doctor of Philosophy in Bioinformatics

Zhejiang University

Hangzhou, China

• Dissertation: Systems biology analyses of molecular mechanisms underlying comorbidity between Parkinson's and Crohn's disease
• Adviser: Prof. Ming Chen (陈铭)

2023 - 2017

Master of Philosophy in Biomedical Engineering

Tianjin Medical University

Tianjin, China

2016 - 2013

• Dissertation: Biochemical pathway and protein-protein interaction network based analyses of genes associated with Parkinson's disease
• Adviser: Prof. Ju Wang (王举)

Bachelor of Science in Biomedical Engineering

Shandong First Medical University
Shandong Academy of Medical Sciences

Taian, China

2013 - 2009

• Dissertation: Comparative study of three MATLAB based methods for retinal image brightness and contrast adjustment
• Adviser: Prof. Yongxin Guo (郭永新)

Bioinformatics Society of Zhejiang Province of China, Membership

Bioinformatics Society of Zhejiang Province of China

N/A

2025 - 2017

Zhejiang University Award of Honor for Graduate

Zhejiang University

N/A

2019

Zhejiang University First-Class Scholarship for Doctoral Mid-term Examination

Zhejiang University
Scholarship amount: ¥ 20,000

N/A

2018

Zhejiang University Award of Honor for Graduate

Zhejiang University

N/A

Zhejiang University Excellent Doctoral Freshman Scholarship

Zhejiang University
Scholarship amount: ¥ 10,000

N/A

2017

Second-Class Prize for Excellent Poster

The 6^th National Conference on Bioinformatics & Systems Biology of China (第六届全国生物信息学与系统生物学学术大会)
Prize amount: ¥ 400

N/A

2014

Shandong First Medical University Excellent Undergraduate Thesis Award

Shandong First Medical University
Shandong Academy of Medical Sciences

N/A

2013

Shandong First Medical University Second-Class Scholarship

Shandong First Medical University
Shandong Academy of Medical Sciences

N/A

2011

Shandong First Medical University Third-Class Scholarship

Shandong First Medical University
Shandong Academy of Medical Sciences

N/A

2010

Science China-Life Sciences

Impact Factor: 8.0

N/A

# 1

Bioinformatics

Impact Factor: 7.6

N/A

# 2

International Journal of Intelligent Systems

Impact Factor: 5.9

N/A

# 3

Molecular Neurobiology

Impact Factor: 5.1

N/A

# 4

Frontiers in Neuroscience

Impact Factor: 4.3

N/A

# 5

Scientific Reports

Impact Factor: 4.3

N/A

# 6

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Impact Factor: 3.6

N/A

# 7

Frontiers in Neurology

Impact Factor: 3.3

N/A

# 8

PLOS ONE

Impact Factor: 3.3

N/A

# 9

Journal of Molecular Neuroscience

Impact Factor: 2.8

N/A

# 10

Mammalian Genome

Impact Factor: 2.7

N/A

# 11

Computational Biology and Chemistry

Impact Factor: 2.6

N/A

# 12

BMC Medical Genomics

Impact Factor: 2.5

N/A

# 13

BMC Neurology

Impact Factor: 2.5

N/A

# 14

Current Bioinformatics

Impact Factor: 2.4

N/A

# 15

Cell Biochemistry and Biophysics

Impact Factor: 2.0

N/A

# 16

BMC Genomic Data

Impact Factor: 1.9

N/A

# 17

Decrypting human biological pathway crosstalk landscape in a deep learning architecture

To Appear on bioRχiv.

N/A

2025

YS Hu^#, Y Chen^#, Y Hu, M Chen*

AWmeta empowers adaptively-weighted meta-analysis for gene expression data

To Appear on bioRχiv.

N/A

N/A

YS Hu, Z Wang, Y Hu, M Chen*

Systems biology framework unravels molecular substrates underlying comorbidity between Parkinson's and Crohn's disease

To Appear on medRχiv.

N/A

N/A

YS Hu, B She, Z Yin, X Yu, W Wu, M Chen*

HPInet: Interpretable prediction of Host-Pathogen protein–protein Interactions using a transformer-based neural network

Under Review, Briefings in Bioinformatics.

Impact Factor：7.9

N/A

YM Hu^#, LY Liu^#, YY Zhu^#, EY Liu, HY Chao, SD Li, C Feng, YS Hu, YH Chen, S Zhang, Y Chen, L Xie, Y Wang, M Chen*

Improved Prediction of Bacterial Type VI Secretion Effector Proteins Using an Integrated Convolutional Neural Network Model Combining N-terminal Signal Sequences, Evolutionary Information and Pre-Trained Protein Language Features

Under Review, mSystems.

Impact Factor：6.1

N/A

YM Hu^#, MQ Yan^#, Y Zhu, H Chao, S Li, Q Ni, YS Hu, EY Liu, LY Liu, Y Chen, Z Zhou, Y Chen, S Zhang, Y Wang, C Feng*, M Chen*

Benchmarking alternative polyadenylation detection in single-cell and spatial transcriptomes

bioRχiv. 2024.10.15.618405. (Under Review, Genome Biology)

N/A

2024

S Li, Z Wang, YS Hu, Q Ni, C Feng, Y Hu, S Zhang, M Chen*

ncPlantDB: a plant ncRNA database with potential ncPEP information and cell type-specific interaction

Nucleic Acids Research. 2024, gkae1017.

Impact Factor: 16.6

N/A

L Liu^#, E Liu^#, Y Hu, S Li, S Zhang, H Chao, YS Hu, Y Zhu, Y Chen, L Xie, Y Shen, L Wu, M Chen*

Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition

BMC Biology. 2024, 22(1):143.

Impact Factor: 5.4

N/A

C Feng^#, RX Tie^#, SG Xin^#, YH Chen, SD Li, YF Chen, XT Hu, YC Zhou, YJ Liu, YM Hu, YS Hu, H Pan, ZX Wu, HY Chao, SL Zhang, QY Ni, J Huang, W Luo*, H Huang*, M Chen*

HALD, a human aging and longevity knowledge graph for precision gerontology and geroscience analyses

Scientific Data. 2023, 10(1):851.

Impact Factor: 8.9

2023

Z Wu^#, C Feng^#, YS Hu, Y Zhou, S Li, S Zhang, Y Hu, Y Chen, H Chao, Q Ni, M Chen*

CoGO: a contrastive learning framework to predict disease similarity based on gene network and ontology structure

Bioinformatics. 2022, 38(18):4380-4386.

Impact Factor: 7.6

2022

Y Chen^#, YS Hu^#, X Hu, C Feng, M Chen*

CoVM²: Molecular Biological Data Integration of SARS-CoV-2 Proteins in a Macro-to-Micro Method

Biomolecules. 2022, 12(8):1067.

Impact Factor: 5.4

N/A

H Chen, X Hu, YS Hu, J Zhou, M Chen*

LBD: a manually curated database of experimentally validated lymphoma biomarkers

Database. 2022, Volume 2022, baac051.

Impact Factor: 4.2

N/A

B Tan, S Xin, YS Hu, C Feng*, M Chen*

PncStress: a manually curated database of experimentally validated stress-responsive non-coding RNAs in plants

Database. 2020, Volume 2020, baaa001.

Impact Factor: 4.2

2020

W Wu, Y Wu, D Hu, Y Zhou, YS Hu, Y Chen, M Chen*

The inflammatory cytokine IL-6 induces FRA1 deacetylation promoting colorectal cancer stemness and malignancy

Oncogene. 2019, 38:4932-4947.

Impact Factor: 7.5

2019

T Wang, P Song, T Zhong, X Wang, X Xiang, Q Liu, H Chen, T Xia, H Liu, Y Niu, YS Hu, L Xu, Y Shao, L Zhu, H Qi, J Shen, T Hou, R Fodde*, J Shao*

Analyzing the genes related to Alzheimer’s disease via a network and pathway-based approach

Alzheimer's Research & Therapy. 2017, 9(1):29.

Impact Factor: 9.2

2017

YS Hu, J Xin, Y Hu, L Zhang*, J Wang*

Network and Pathway-Based Analyses of Genes Associated with Parkinson’s Disease

Molecular Neurobiology. 2017, 54(6):4452-4465.

Impact Factor: 5.1

N/A

YS Hu, Z Pan, Y Hu, L Zhang*, J Wang*

Detecting pathway relationship in the context of human protein-protein interaction network and its application to Parkinson’s disease

Methods. 2017, 131:93-103.

Impact Factor: 4.2

N/A

Y Hu, Y Yang, Z Fang, YS Hu, L Zhang*, J Wang*

GRONS: a comprehensive genetic resource of nicotine and smoking

Database. 2017, Volume 2017, bax097.

Impact Factor: 4.2

N/A

Z Fang, Y Yang, YS Hu, MD Li*, J Wang*

Analyzing the genes related to Alzheimer’s disease via a network and pathway-based approach

The 1^st Sino-Russian Workshop on Integrative Bioinformatics and Systems Biology (WIBSB-2018)

Novosibirsk, Russia

2018

Network and pathway based analyses of genes associated with Parkinson’s disease

The 7^th National Conference on Bioinformatics and Systems Biology of China

Chengdu, China

2016

Uncovering the common pathogenesis in neurodegenerative and psychiatric disorder via network approaches

The 7^th National Conference on Bioinformatics and Systems Biology of China

Chengdu, China

N/A

Identifying the enriched biological pathways in genes related to nicotine dependence via a network-based gene-weighting algorithm

The 7^th National Conference on Bioinformatics and Systems Biology of China

Chengdu, China

N/A

Common characteristics of Alzheimer’s disease and Parkinson’s disease based on AlzGene and PDGene databases

The 6^th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

2014

Computing the phenotype similarity based on OMIM database and MESH vocabulary

The 6^th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

N/A

TarPriGO: a new method to prioritize miRNA targets based on Gene Ontology

The 6^th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

N/A

A comprehensive pathway and network analysis of candidate genes associated with nicotine addiction

The 6^th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

N/A

The functional divergence analysis of neuronal nicotinic acetylcholine receptor subunits

The 6^th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

N/A

Zhejiang University-Bielefeld University Joint Symposium

Talk Title: Analyzing the genes related to Alzheimer’s disease via a network and pathway-based approach

Bielefeld, Germany

2019

First Sino-Russian Workshop on Integrative Bioinformatics and Systems Biology (WIBSB-2018)

Talk Title: Analyzing the genes related to Alzheimer’s disease via a network and pathway-based approach

Novosibirsk, Russia

2018

Network and pathway based analyses of genes associated with Parkinson’s disease

The 7^th National Conference on Bioinformatics and Systems Biology of China

Chengdu, China

2016

Common characteristics of Alzheimer’s disease and Parkinson’s disease based on AlzGene and PDGene databases

The 6^th National Conference on Bioinformatics and Systems Biology of China

Nanjing, China

2014

一种生化通路串话识别方法 (Chinese Patent)

Inventor: 陈铭，胡言石 (Yan Shi HU)，陈俞皓

Application Number: 2023107816823
Filing Date: 2023-06-28
Publication number: CN116959588A
Publication Date: 2023-10-27

N/A

2023